Updates made to the www.psort.org site will be reported here, as well
as on the psort-update mailing list. To subscribe to the mailing list
to automatically receive major updates, email maillist@sfu.ca with "subscribe psort-update"
in the subject or body of the message. To unsubscribe, enter "unsubscribe
psort-update" in the subject or body of email.

We have released a Docker version of the PSORTb
web service, it can be installed from Github. Docker allows you
to quickly install a local version of the PSORTb web service on
your own machine and run proteins locally. (what is docker?)

A major windstorm caused power outages all over the city on the evening of Monday, November 21,
disrupting PSORTb service due to server switch problems. The problem was fixed by the end of Tuesday, November 22nd.
PSORTb services are now back online.

We have upgraded PSORTb with a new version of SCLBLASTdb with added proteins to optimize software accuracy/recall. The new update (v3.0.2) should be the stable version and we strongly encourage you to use this version for your computations.

18th May 2010: PSORTb bug fixed

The bug detected in the new PSORTb 3.0 version has
been fixed as of May 18, 2010. This was a
serious error that resulted in incorrect predictions
being made versus the version published in the
associated paper. Therefore please
only use this correct version, which we will now
refer to now as 3.0.1. We are
currently updating the precomputed genome results
accordingly. We sincerely apologize for any
inconvenience caused by this notable error.

17th May 2010: Serious error in predictions found

A significant error was found in the results newly release
PSORTb v3.0 causing some proteins to be incorrectly predicted. We
have taken the tool offline while we implement the fix and don't
anticipate the outage to be long.

14th May 2010: website down due to campus-wide power outage

Due to a significant power upgrade affecting the entire Burnaby campus at SFU, including all emergency power, www.psort.org and db.psort.org will have a scheduled shutdown from Friday, May 14 to Monday, May 17, 2010. We apologize in advance for the inconvenience.

Wow, you all really like us! Due to an overwhelming volume of
usage on the new PSORTb v3 we've been having some growing pains
which have resulted in some analysis failing. We've made some
changes to allow longer running times before timeouts occur. For
sequence files larger than 100k we are still requiring people use
the new email results feature. Happy PSorting!

28th December 2009: Errors with PSORTb v.3 web server resolved

As with all new software, just when you think all the bugs are
worked out, users discover issues you missed. We have fixed some
issues with PSORTb 3 and Internet Explorer when it comes to
selecting advanced options and receiving results by email. We also
fixed a minor bug with BLAST files not being cleaned up properly
in our backend server causing requests to fail. Sorry for any inconvenience, and please
let us know if you continue to experience any issues with the
website. Thanks.

18th December 2009: PSORTb v3 web server now available

We are excited to announce that PSORTb v.3 is now online with much improved features! It can be accessed at www.psort.org/psortb. A freely available command-line version can also be downloaded here. Please contact us at psort-mail@sfu.ca if you notice any problems or have trouble installing the software.

2nd April 2009: Update of PSORTb to address
incompatibility with Bioperl 1.6.0

A change in how Bioperl's StandAloneBlast module with the release
of Bioperl 1.6.0 caused PSORTb to crash upon execution. We've
rewritten the PSORTb SCLBlast module to handle the new version of
Bioperl while also remaining backwards compatible with older version
of Bioperl. The new version can be found in our downloads section.

- The Precomputed Genomes page has been updated. See db.psort.org/updates.html for a list of newly added PSORTb precomputed genomes.
- psort.org Resources page has been updated. The list of links locally hosted resources has been moved to the top of the webpage for more convenient access.

3rd December 2007: New resource links for psort.org

The following new prediction tools and databases have been added to the
Resources page:

New links for various prediction tools and databases published in 2006-2007
have been added to the Resources page.

20th April 2007: New version of PSORTb released

A new version of standalone PSORTb has been released in the downloads section.
This version does not require the installation of HMMTOP. We have also noticed a slight incompatibility between PSORTb 2.0.6
(the previous stable release) and the new Mac OSX 10.4. We are working to fix this problem.

28th December 2006: Scheduled downtime

www.psort.org is unavailable all day due to scheduled server maintenance. We apologize for the inconvenience.

28nd November 2006: Power Outage at Simon Fraser University

We appologize that due to a snow storm the power was knocked out at Simon Fraser University the evening of Sunday November 26th. The servers running PSORTb were not brought back online until mid-day on Monday November 27th. We appologize for the inconvenience.

18nd October 2006: Bug fix in web version of PSORTb

We have fixed a minor bug in the web version of PSORTb that caused results to be flagged as having possible multiple localizations if a signal peptide was detected. This bug was introduced in late August and only effected the web version, not the stand alone version.

22nd September 2006: New beta version of PSORTb available

We are aware that the HMMTOP website seems to be undergoing upgrades for a new software version. We have not tested whether or not version 2.9 is compatible with the current PSORTb v2.0.
Regardless, we have created a beta version of PSORTb that does not require the HMMTOP module. Please contact
psort-mail@sfu.ca if you would like to try out this new version of our software.

19th September 2006: Datasets of Proteins of Known Localizations page updated

PSORTb v.2.0.5 has been made available at the PSORTb
Downloads Page. This version eliminates a naming conflict between
PSORTb's Profile package and a BioPerl package of the same name.

27th July 2005: Feedback form removed

We have removed the feedback form from the Contact
Us page to prevent hijacking of the form by spammers.
Please use
psort-mail@sfu.ca to
contact
us instead. We welcome your comments, suggestions and
questions, and
we'll try and respond as quickly as possible!

19th July 2005: New Links Added

We have updated the PSORT.org
Index Page with a number of links to recently-released
predictive
methods and databases. We have also added a section containing
links
to beta-barrel outer membrane protein predictors.

2nd May 2005: Brief Downtime

The PSORT.org site was down briefly on the
morning
of Saturday, April 30th due to a scheduled power outage. The
system
was quickly brought back up online, however we apologize for
any inconvenience
the downtime may have caused.

PSORTb v.2.0.4 has been made available at the
PSORTb
Downloads Page. This version supresses HMMTOP warning
messages
that certain users have experinced when running standalone
PSORTb,
and has been slightly edited to emphasize the workaround for
the Bioperl/BLAST
incompatibility that is required for standalone PSORTb to work
under
certain systems.

19th February 2005: Brief Downtime

The PSORT.org site was down briefly on the
morning of
Saturday, February 19th due to a scheduled power outage. The system was
quickly brought back up online, however
we apologize for any inconvenience the downtime may have caused.

PSORTb v.2.0.3 has been implemented on the web
subsmission form and is available from the PSORTb
Downloads Page. This version fixes an error in earlier
versions
in which a multiple localization flag was incorrectly appended
to
a predicted site when, in fact, the score distribution and
BLAST results
did not support potential multiple sites.

The 2005 edition of the Nucleic
Acids Research Database Issue is out, and features several
databases
relevant to subcellular localization. Links to the databases
and the
articles describing them have been added to the PSORT.org
Index Page, under the section "Other subcellular
localization
databases". This new section on the resources list
replaces the
"Datasets from other sources" link on the Datasets
page,
which now only contains links to archived versions of the
PSORTb training
data. We do recommend, however, that you ignore the
aforementioned
Datasets page in favour of our new PSORTdb
site. It contains both training data and predicted data in an
easily
browsable/queryable databse format, and will make the
construction
of your training datasets much, much, much easier.

Also, PSORTb wishes you a happy 2005, full of
good
times and correctly predicted localization sites.

24th November 2004: Updates to the Precomputed Genomes
Pages

In order to better integrate the PSORTb
website and
the PSORTdb website, we have
made
some updates to the Precomputed Genomes pages. The PSORTb
v.2.0 Precomputed Genomes page now dynamically retrieves
both
the input FASTA files and the tab-delimited PSORTb results
from PSORTdb.
The URL for this page has not changed since the Oct. 22
update. The
archived PSORTb v.1.1.2 Genomes page now has a new URL:http://www.psort.org/oldpsortbversion1/genomes.pl.
This page has also been updated to allow dynamic retriveal of
files
from PSORTdb.

23rd November 2004: Correction to v.2.0.2 Filename and
About
that Pesky BLAST Problem

We have receieved some inquiries regarding
the problem
occurring between Bioperl and the SCL-BLAST module. In Solaris
(SPARC
and x86), Mac OSX, and certain Linux distributions, even
though BLAST
is working properly, the system call to BLAST returns a -1
return
code and an error is returned. We have developed a workaround
to this
problem, which involves commenting out the line in which the
blastall
return code is checked. To apply this workaround, comment out
the
line:

We have successfuly ported the command-line
version
of PSORTb v.2.0.2 to the Solaris operating system. The source
code,
along with the necessary prerequisite modules, is available at
the
PSORTb Downloads Page.

Version 0.09 of the Algorithm::SVM prerequisite
module
has replaced version 0.08 on the PSORTb Downloads Page. This new version
fixes
a bug in previous versions wherein an uninitialized variable
was causing
sporadic problems upon instantiation of the module.

22nd October 2004: New URL for the Precomputed Genomes
Page

PSORTb's Precomputed Genomes Page, previously
located
at www.psort.org/genomes/index.html, has been moved to http://www.psort.org/genomes/genomes.pl
in order to facilitate the addition of new genomes. The
index.html
page will now redirect you automatically to this new page,
however
we recommend that you update your bookmarks to the new
address. Please
explore PSORTdb's cPSORTdb
dataset
as an alternative to the precomputed genomes page too! It
offers all
of the precomputed genomes with a user interface that allows
for querying
of the database through text, browsing, or BLAST, and for
flexible
display and downloading of the data.

20th October 2004: Standalone PSORTb for Mac OSX
released

We have successfuly ported the command-line
version
of PSORTb v.2.0 to the Mac OSX operating system. The source
code,
along with the necessary prerequisite modules, is available at
the
PSORTb Downloads Page.

In reponse to a survey reply, we have also
added
a link to the PSORTb Results page header, which takes the user
to
the explanation of the different output formats in the
Documentation
section.

26th August 2004: Minor updates to PSORTb
site

Several minor updates have been made to the
PSORTb
site over the last few days. A brief guide to submitting
sequences
using the standalone version of PSORTb has been added as
section 5.3
of the Documentation.
A quick
survey has been added to the PSORTb Downloads page to collect feedback
regarding
PSORTb's utility and functions you would like to see
added/changed/deleted.
The INSTALL and README files associated with the
standalone version
have also been updated - though the files describe
installation of
the latest version of PSORTb (v.2.0), the version was
mistakenly labelled
as 1.1.4. These typos have been corrected.

12th August 2004: PSORTdb v.1.0 released

A new member
has been
added to the PSORTb family!

PSORTdb
v.1.0 (http://db.psort.org)
has now been released. PSORTdb is a comprehensive database of
bacterial
protein subcellular localization comprising ePSORTdb - a set
of ~2000
proteins whose localization has been experimentally verified -
and
cPSORTdb - a database containing PSORTb predicted
localizations for
140 bacterial species. Extensive annotation is available for
each
entry in the database.

PSORTdb allows users to search the
annotations via
simple text queries, advanced text queries, or by BLAST, and
it alsow
allows hierarchical browsing of entries. The results of
searches can
be extensively customized, and can be downloaded in tab
delimited
text or FASTA format.

We hope that PSORTdb will become a valuable
resource
for researchers interested in creating their own custom
datasets,
as well as users who would like to answer questions regarding
bacterial
protein localization. We invite you to explore PSORTdb and we
welcome
any comments or
suggestions
you may have.

17th June 2004: PSORTb v.2.0 released

PSORTb v.2.0 has been released!

On
behalf
of the PSORTb development team, I'd like to announce that an
updated
and expanded version of PSORTb is now available at http://www.psort.org/psortb. This new version
replaces
v.1.1 and offers users increased predictive coverage and the
ability
to analyze both Gram-negative and Gram-positive proteins. You
might
also notice a change in name - recognizing that the hyphen in
the
original PSORT-B name may cause pattern recognition problems
in certain
instances, we have renamed the program PSORTb!

The documentation available on this
website has
been updated to reflect the new version of PSORTb, and precomputed genomes are available using
v.2.0. A
reference to the new version will be added when it comes
available.

PSORTb is always undergoing development, with the goal of
improving
both the program and the website, and we'd appreciate your
suggestions
to assist us in the development of future versions. Please
contact
us with any comments, suggestions, or questions you may have.
We can
be reached by email at psort-mail@sfu.ca, or through a form
available
at http://www.psort.org/psortb/contact.pl.

Thank you for your interest in PSORTb, and we hope that the
program
will be an exciting and valuable addition to your
research!

5th February 2004: Standalone PSORT-B 1.1.4 for Linux
released

A standalone version of PSORT-B for the Linux
platform
has been released. The code and documentation is available at
the
new PSORT-B Downloads page. Version 1.1.4
incorporates
an exact match feature into the SCL-BLAST module, such that if
your
protein exactly matches one in our database, a prediction will
be
rteurned instantly without having to utilize other modules.
Presently
the webserver still utilizes v.1.1.2, which does not contain
this
exact match filter.

16th December 2003: Notice of downtime

PSORT-B will be unavailable briefly on the
morning
(PST) of Wednesday, 17th December, 2003, due to a scheduled
hardware
upgrade. The service will be restored that afternoon.

3rd July 2003: Maximum file/sequence size

To help control the load on our servers, we have placed a
limit on
the maximum file size and the length of the submitted
sequences that
can be sent to our servers. Currently, the limit has been set
to 300,000
bytes.

26th June 2003: Difficulties with sequence submission
resolved

This problem with some sequence submissions has been
resolved. Thank
you for your understanding.

25th June 2003: Difficulties with sequence submission
detected

Some users may have encountered difficulties
submitting
sequences - typically the request would time out and not
return any
results. We are currently examining this further. We apologize
for
any inconvenience.

23rd June 2003: PSORT-B RefSeq genomes go
online

The PSORT-B Precomputed Genomes page, at http://www.psort.org/genomes, now contains
the results
of PSORT-B analyses for several bacterial genomes. The input
genomes
used are NCBI RefSeqs, and the input files are available on
the page
as well.